Bioinformatics support for the Baker Institute: team and projects update

Domain Bioinformatics

Sergio Ruiz Carmona, Artika Nath and Rodrigo Canovas September 2021

Provide Support Role for all Baker Laboratories

Started

2017

-Project work

-Grant applications -Consultations

2021

❖3 Bioinformaticians

❖35 projects – completed

●Data analysis

●5 grant applications

●4 manuscripts published

❖17 projects – ongoing

●5 manuscripts in preparation

●1 manuscript submitted

Major underpinning ANALYTICS infrastructure for Baker

MISSION: To build bioinformatics capacity at the Baker Institute through collaboration, support and training

CAPABILITES: Analysis of data and cross-omic integration from diverse technologies:

•Genomics

•Epigenomics

•Transcriptomics (Bulk & single cell)

•Proteomics

•Metabolomics

•Metagenomics

•Blood cell traits

APPROACHES:

•Statistical analysis

•Machine learning

•Network analysis

•High dimensional data normalisation, processing & visualisation

•Design of computational algorithms

Who we are

Artika Nath

●PhD in Bioinformatics (University Of Melbourne)

○Integrative genomics

○Functional analysis

○Network/Cluster analysis

○Data & Statistical Analysis

○Gene expression analysis (Bulk & Single Cell)

○GWAS (Univariate & Multivariate)

○eQTL and Colocalisation Analysis

●Postdoctoral Researcher / Bioinformatician (Baker)

○Since 2018

○Integrative genomics

○Data science, manipulation, visualisation

○Analysis of transcriptomics, metabolomics, protein data

○UK-Biobank Related projects

●Cambridge Baker Systems Genomics Initiative

○Co-Lead on the INTERVAL RNA-Seq project

○5000 samples with RNA-seq data

○eQTL analysis, colocalisation analysis, coexpression network analysis, Integration with other molecular traits

Nath et al., 2019

Nath et al., 2017

Nath et al., 2019

Nath et al., 2019

Investigate the transcriptomic profile of reduced cardiac O-GlcNAcylation in the diabetic heart

Excessive O-GlcNAcylation is suspected to contribute to myocardial dysfunction in diabetes

The global transcriptomic profile of

Collaboration - Darnel Prakoso

 

Prof. Rebecca Ritchie’s Lab

 

OGA-treated diabetic mice is similar

 

 

 

 

 

 

to non-diabetic mice

 

 

 

 

Non-Diabetic

 

 

 

 

 

 

 

 

Diabetic

Diabetic - OGA

OGA - reduces O-GlcNAcylation

 

 

 

Enrichment analysis revealed that

 

 

 

OGA administration altered pathway

 

 

 

associated with cardiac remodelling.

Fffffffffffffffi

 

i

 

 

Prakoso, Nath, et al - Manuscript in Prep.

Rodrigo Cánovas

●PhD - Engineering, The University of Melbourne, Australia

○In the disciplines of Bioinformatics Software and Coding and Information Theory

○Finished in 2015

○Practical Compression for Multi-Alignment Genomic Files

●Postdoctoral Researcher, LIRMM and IBC, France

○From 2015 to end of 2017

○ Developing algorithms for analysing next-generation sequencing data

●Research Officer / Bioinformatician, Baker Institute, Australia

○Since 2018, Systems Genomics lab

○Genomic risk prediction

○Data science, manipulation and visualization

●Bioinformatics and Computer Science including, between others:

○Genomic risk prediction, survival analysis, design and analysis of algorithms and data structures, indexing, compression, pattern matching , machine learning, deep learning, data analysis

COVID-19 and venous thromboembolism disease (VTE) association

(Status: manuscript of exploratory analysis )

Among UK Biobank participants who were COVID-19 tested we are exploring the following research questions:

I.Does the predictors of genetic predisposition for VTE helps to predict the development of COVID-19?

II. Considering only individuals that tested positive. Are predictors of genetic predisposition for VTE associated with an increase in the mortality rate from COVID-19?

III. Association of COVID-19 with developing VTE disease

Collaboration with Baker’s Atherothrombosis and

Vascular Biology Lab:

Hannah Stevens

Dr James McFadyen

Parameters Correlation plot

Predicting Covid-Status

RDH11 target role in humans

Collaboration with Baker’s Lipid Metabolism and

Cardiometabolic Disease Lab:

Dr Michael Keating

Among the UK Biobank:

I.Understand what role that RDH11 might be playing in humans

II.Check if RDH11 is associated with phenotypes linked to these pathways A. (eg. phenotypes associated with variation at the RDH11 locus)

Sergio Ruiz Carmona

●PhD in Computational Biology and Drug Discovery

○Finished in 2017 in Barcelona (Spain)

○Method development and applications in drug design

●Postdoc in drug discovery for blood disorders

○In Barcelona (Spain)

○Drug patent & spin-off to progress into clinical trials

○EMBO short-term fellow in Pharmacogenomics

●Research Officer / Bioinformatician @Baker Institute

○Since early 2019, Systems Genomics lab

○Protein structure genomics

○Data science, manipulation and visualization

○Bioinformatics and gene expression analysis

○Machine learning and High Performance Computing

○UK Biobank

○Web development and interactive applications / dashboards

Oxygen Pathway analysis in CTEPH patients

Collaboration with the

Sports Cardiology Lab

Dr. Erin Howden

Dr. Guido Claessen

A/Prof Andre La Gerche

Interactive

Shiny App

Baker quarterly publication award (presentation next Tuesday, 7th)

lncRNAs in physiological and pathological hypertrophy

Collaboration with the

Cardiac Hypertrophy Lab

Dr. Jenny Ooi

Prof. Julie McMullen

TrainingPeaks - Athlete data analysis

~200 athletes

60.000 training activities

Collaboration with the

Sports Cardiology Lab

Kristel Janssens

Dr. Guido Claessen

A/Prof Andre La Gerche

How does it work?

○How can Baker researchers engage with us?

○How does the process look like?

○What can you expect from us?

How much is it?

We work with a collaborative model

-Authorship in papers

-Grant participation

-General advice

Project requests

https://intranet.baker.edu.au/resear ch-resources/platform-

technologies/bioinformatics- program/domain-bioinformatics/

Search

“Domain Bioinformatics”

on the intranet search box

Research resources >

Platform Technologies >

Bioinformatics Program >

Domain Bioinformatics

Request & project timeline

First email

Initial

Initial

Meeting

analysis &

request

(Full team)

report

 

Updated

Follow-up

analysis &

Meetings

report

 

Ideal situation

Background

Ideal

information

Outcome

Data

analysis

Also...

UK Biobank Projects

Recruited Individuals

Recruited ~500,000 UK individuals (not families) between 2006 – 2010

Image obtained from the UKB webpage

UK Biobank Timeline

Covid-19

DataNightingale Health’s study

Blood samples

120,000

20202021

Exome

sequencing of

200,000

Image adapted from R. Collins UKB slides

Principles of accessing UK Biobank

●Open access resource, available for bona fide researchers to conduct health-related research that is in the public interest

●Researchers are obliged to return their results to UK Biobank so they can be shared with others

●Any work/presentation/publication must include the following phrase:

“This research has been conducted using the UK Biobank Resource under application number 55469”

Using the Baker-wide UKB project #55469

●Access the UK Biobank

○Register with the UK Biobank

■https://www.ukbiobank.ac.uk/enable-your-research/register

○Contact Mike Inouye or Domain Bioinformatician Team to:

■Be added to Baker’s approved UKB project

●Rules of how to use the UKB data:

○If you have data science training specific arrangements can be made to grant access to the data

○All UKB data must be and remain on the server (common Baker cluster)

○NO UKB DATA IS TO BE TRANSFERRED OFF THE SERVER

Using the Baker-wide UKB project #55469

●Suggested Project Pipeline:

○Request access to the UKB

○Explore what have been done already

○Submit a project request to the Domain Bioinformatics group

○Before the first meeting check on the UKB showcase which data would be useful

■Some links that may help:

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○Create some amazing research

○Report results back to the UK Biobank

Thank you!

bioinformatics@baker.edu.au

Domain Bioinformatics

Sergio Ruiz Carmona, Artika Nath and Rodrigo Canovas September 2021